BOGOTA, Aug 6 (Reuters) - A Colombian high court on Wednesday ruled that Marxist rebels found guilty of war crimes cannot hold public office, a decision that would block FARC leaders from entering politics and may complicate negotiations to end five decades of war.

The ruling by the constitutional court throws into doubt agreements reached between the government and leaders of the Revolutionary Armed Forces of Colombia (FARC) which laid the groundwork for rebel political participation if the two sides agree on peace terms.

President Juan Manuel Santos will be sworn in to office on Thursday after winning a second term mostly on the back of his bid to end the conflict that has killed more than 200,000 and displaced millions.

Santos launched peace talks with the FARC at the end of 2012 with massive popular backing, but months of negotiations amid ongoing war and continued rebel attacks against civilian targets has dimmed support and left many questioning if the guerrillas should be allowed to hold office.

The court ruled that only rebels who have been involved in lesser crimes can seek election to political office. Congress must decide what constitutes such crimes, Luis Ernesto Vargas, president of the court, told reporters.

The decision may please some critics of the peace talks, most notably former President Alvaro Uribe who has expressed outrage that FARC crimes could go unpunished and that rebel commanders may end up with seats in Congress.

The FARC has not yet responded publicly to the court ruling, but has previously rejected the idea of serving any jail time.

FARC political participation is one item on a five-point agenda that the two sides have already agreed. The details of the accord have not been made public.

They also have agreed on terms of land reform and how to end the illegal drug trade. Still to be discussed is the complex issue of reparation to victims and how to end the conflict. (Reporting by Helen Murphy and Luis Jaime Acosta; Editing by Lisa Shumaker)